# HG changeset patch
# User nick
# Date 1450727268 18000
# Node ID 7f513b9b1b1e4e6a8602ec8abeb3eaf1367f6b66
# Parent  aedbdf8ce1afdc7a640156d2cc661bc34692605c
Change names to dunovo, use newer Github release.

diff -r aedbdf8ce1af -r 7f513b9b1b1e align_families.xml
--- a/align_families.xml	Tue Dec 08 08:59:27 2015 -0500
+++ b/align_families.xml	Mon Dec 21 14:47:48 2015 -0500
@@ -1,10 +1,11 @@
 <?xml version="1.0"?>
-<tool id="align_families" name="Du Novo: Align families" version="0.2">
+<tool id="align_families" name="Du Novo: Align families" version="0.3">
   <description>of duplex sequencing reads</description>
   <requirements>
     <requirement type="package" version="7.221">mafft</requirement>
-    <requirement type="package" version="0.2">duplex</requirement>
+    <requirement type="package" version="0.3">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <!-- TODO: require Python 2.7 -->
   </requirements>
   <command detect_errors="exit_code">python \$DUPLEX_DIR/align_families.py -p \${GALAXY_SLOTS:-1} $input &gt; $output
   </command>
diff -r aedbdf8ce1af -r 7f513b9b1b1e dunovo.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dunovo.xml	Mon Dec 21 14:47:48 2015 -0500
@@ -0,0 +1,62 @@
+<?xml version="1.0"?>
+<tool id="duplex" name="Du Novo: Make consensus reads" version="0.3">
+  <description>from duplex sequencing alignments</description>
+  <requirements>
+    <requirement type="package" version="0.3">duplex</requirement>
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
+    <!-- TODO: require Python 2.7 -->
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+    python \$DUPLEX_DIR/dunovo.py -r $min_reads -q $qual_thres -F $qual_format $input
+    #if $keep_sscs:
+      --sscs-file $sscs
+    #end if
+    > duplex.fa
+    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1
+    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2
+  ]]>
+  </command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Aligned input reads" />
+    <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
+    <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
+    <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
+      <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
+      <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
+    </param>
+    <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" />
+  </inputs>
+  <outputs>
+    <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
+    <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
+    <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)">
+      <filter>keep_sscs</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="families.msa.tsv"/>
+      <output name="output1" file="families.cons_1.fa"/>
+      <output name="output2" file="families.cons_2.fa"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
+
+-----
+
+**Input**
+
+This expects the output format of the "Align families" tool.
+
+-----
+
+**Output**
+
+This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
+
+    </help>
+</tool>
diff -r aedbdf8ce1af -r 7f513b9b1b1e duplex.xml
--- a/duplex.xml	Tue Dec 08 08:59:27 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-<?xml version="1.0"?>
-<tool id="duplex" name="Du Novo: Make consensus reads" version="0.2">
-  <description>from duplex sequencing alignments</description>
-  <requirements>
-    <requirement type="package" version="0.2">duplex</requirement>
-    <requirement type="set_environment">DUPLEX_DIR</requirement>
-  </requirements>
-  <command detect_errors="exit_code"><![CDATA[
-    python \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input
-    #if $keep_sscs:
-      --sscs-file $sscs
-    #end if
-    > duplex.fa
-    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1
-    && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2
-  ]]>
-  </command>
-  <inputs>
-    <param name="input" type="data" format="tabular" label="Aligned input reads" />
-    <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/>
-    <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/>
-    <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+">
-      <option value="sanger" selected="true">Sanger (PHRED 0 = &quot;!&quot;)</option>
-      <option value="solexa">Solexa (PHRED 0 = &quot;@&quot;)</option>
-    </param>
-    <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" />
-  </inputs>
-  <outputs>
-    <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/>
-    <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/>
-    <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)">
-      <filter>keep_sscs</filter>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-      <param name="input" value="families.msa.tsv"/>
-      <output name="output1" file="families.cons_1.fa"/>
-      <output name="output2" file="families.cons_2.fa"/>
-    </test>
-  </tests>
-  <help>
-
-**What it does**
-
-This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families.
-
------
-
-**Input**
-
-This expects the output format of the "Align families" tool.
-
------
-
-**Output**
-
-This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file.
-
-    </help>
-</tool>
diff -r aedbdf8ce1af -r 7f513b9b1b1e make_families.xml
--- a/make_families.xml	Tue Dec 08 08:59:27 2015 -0500
+++ b/make_families.xml	Mon Dec 21 14:47:48 2015 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="make_families" name="Du Novo: Make families" version="0.2">
+<tool id="make_families" name="Du Novo: Make families" version="0.3">
   <description>of duplex sequencing reads</description>
   <requirements>
-    <requirement type="package" version="0.2">duplex</requirement>
+    <requirement type="package" version="0.3">duplex</requirement>
     <requirement type="set_environment">DUPLEX_DIR</requirement>
   </requirements>
   <!-- TODO: Add dependency on coreutils to get paste? -->
diff -r aedbdf8ce1af -r 7f513b9b1b1e tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 08 08:59:27 2015 -0500
+++ b/tool_dependencies.xml	Mon Dec 21 14:47:48 2015 -0500
@@ -3,10 +3,10 @@
   <package name="mafft" version="7.221">
     <repository changeset_revision="d71e007323d4" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="duplex" version="0.2">
+  <package name="duplex" version="0.3">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">https://github.com/makrutenko/duplex/archive/v0.2.tar.gz</action>
+        <action type="download_by_url">https://github.com/makrutenko/dunovo/archive/v0.3.tar.gz</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>